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Genome Composition Plasticity in Marine Organisms

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Genome Composition Plasticity in Marine Organisms Genome Composition Plasticity in Marine Organisms A Thesis submitted to University of Naples “Federico II”, Naples, Italy for the degree of DOCTOR OF PHYLOSOPHY in “Applied Biology” XXVIII cycle by Andrea Tarallo March, 2016 1 University of Naples “Federico II”, Naples, Italy Research Doctorate in Applied Biology XXVIII cycle The research activities described in this Thesis were performed at the Department of Biology and Evolution of Marine Organisms, Stazione Zoologica Anton Dohrn, Naples, Italy and at the Fishery Research Laboratory, Kyushu University, Fukuoka, Japan from April 2013 to March 2016. Supervisor Dr. Giuseppe D’Onofrio Tutor Doctoral Coordinator Prof. Claudio Agnisola Prof. Ezio Ricca Candidate Andrea Tarallo Examination pannel Prof. Maria Moreno, Università del Sannio Prof. Roberto De Philippis, Università di Firenze Prof. Mariorosario Masullo, Università degli Studi Parthenope 2 LIST OF PUBLICATIONS 1. On the genome base composition of teleosts: the effect of environment and lifestyle A Tarallo, C Angelini, R Sanges, M Yagi, C Agnisola, G D’Onofrio BMC Genomics 17 (173) 2016 2. Length and GC Content Variability of Introns among Teleostean Genomes in the Light of the Metabolic Rate Hypothesis A Chaurasia, A Tarallo, L Bernà, M Yagi, C Agnisola, G D’Onofrio PloS one 9 (8), e103889 2014 3. The shifting and the transition mode of vertebrate genome evolution in the light of the metabolic rate hypothesis: a review L Bernà, A Chaurasia, A Tarallo, C Agnisola, G D'Onofrio Advances in Zoology Research 5, 65-93 2013 4. An evolutionary acquired functional domain confers neuronal fate specification properties to the Dbx1 transcription factor S Karaz, M Courgeon, H Lepetit, E Bruno, R Pannone, A Tarallo, F Thouzé, P Kerner, M Vervoort, F Causeret, A Pierani and G D’Onofrio EvoDevo, Submitted 5. Lifestyle and DNA base composition in annelid polychaetes A Tarallo, MC Gambi, G D’Onofri Physiological Genomics, Submitted 3 Abstract The molar ratio of the nucleotides (GC%, i.e. the Guanine+Cytosine content) is well known to evolve through the genomes of all the organisms. Several hypotheses have been drawn out to explain the causes of the nucleotide composition variability among orgnisms. In the Thesis project major attention has been directed to the Metabolic Rate hypothesis (MRh). The main goal was to test if the MRh, first proposed to explain the nucleotide variability within mammalian genomes, could also explain the base composition variability among lower vertebrates and invertebrates. To this aim an extensive analysis of more than two hundred teleostean species has been carried out, followed by a pioneering study of annelid polychaete and tunicate genomes. Regarding teleosts, the results clearly highlighted that environment (i.e. salinity) and lifestyle (i.e. migration) both affect simultaneously the physiology (the metabolic rate), the morphology (the gill area) and the genome composition (GC%). Thus supporting a link between the metabolic rate (MR) and the genome base composition, as expected in the light of the MRh. Moreover, a comparative analysis of completely sequenced teleostean genomes showed that the metabolic rate was correlated not only with the GC content of the genome, but also with the intron structures. Indeed, at increasing metabolic rates introns were shorter and GC-richer. A preliminary analysis of annelids polychaetes showed that motile and sessile species were characterized by different MR and GC%, being both higher in the former than in the latter. The investigation was extended to the well known solitary tunicates, C. robusta and the congeneric C. savignyi. Our data revealed slight but significant morpho-physiological differences between the two species, consistent not only with an ecological niche differentiation, but also with their genomic GC content. All the above results converge towards the same conclusion, thus giving consistency to the MRh as major factor driving the genome base composition evolution of all living organisms. 4 Index List of Abbreviations ....................................................................................................... 8 List of Figures .................................................................................................................. 9 List of Tables.................................................................................................................. 10 Chapter I ........................................................................................................................ 11 INTRODUCTION ............................................................................................................. 11 1.1 BIASED GENE CONVERSION HYPOTHESIS ..................................................... 14 1.2 METABOLIC RATE HYPOTHESIS ..................................................................... 20 1.3 AIMS AND STRATEGIES ................................................................................. 23 Chapter II ....................................................................................................................... 25 INTRODUCTION ............................................................................................................. 25 2.1 GENOME COMPOSITION IN TELEOSTS .......................................................... 25 PART I ............................................................................................................................ 27 2.2 SALINITY AND MIGRATION ............................................................................ 27 RESULTS ......................................................................................................................... 29 2.3 EFFECT OF PHYLOGENY ................................................................................. 29 2.4 WHITHIN GENOME ANALYSIS ....................................................................... 32 2.5 THE EFFECT OF ENVIRONMENT AND LIFESTYLE ........................................... 34 DISCUSSION ................................................................................................................... 41 PART II ........................................................................................................................... 45 2.6 THE GENOME ARCHITECTURE OF TELEOSTS ................................................. 45 RESULTS ......................................................................................................................... 46 2.7 DISTRIBUTION OF THE INTRONIC GC CONTENT............................................ 46 2.8 PAIRWISE COMPARISON ............................................................................... 52 2.9 THE MR IN THE FIVE TELEOSTS ..................................................................... 57 DISCUSSION ................................................................................................................... 60 5 CONCLUSION ................................................................................................................. 62 Chapter III ...................................................................................................................... 64 INTRODUCTION ............................................................................................................. 64 3.1 GENOME COMPOSITION IN POLYCHAETES................................................... 64 3.2 DIFFERENCES IN LOCOMOTION .................................................................... 65 3.3 THE POLYCHAETA GENOME .......................................................................... 66 RESULTS ......................................................................................................................... 67 3.4 METABOLIC RATE IN POLYCHAETES .............................................................. 67 3.5 NUCLEOTIDE COMPOSITION ......................................................................... 67 DISCUSSION ................................................................................................................... 69 3.6 PHYLOGENETIC INDEPENDENCY OF GC% AND METABOLISM ...................... 69 3.7 BACTERIAL CONTAMINATION ....................................................................... 71 CONCLUSION ................................................................................................................. 72 Chapter IV ..................................................................................................................... 73 INTRODUCTION ............................................................................................................. 73 4.1 MORPHO-PHYSIOLOGICAL COMPARISON IN ASCIDIANS .............................. 73 4.2 DIFFERENCES BETWEEN C. robusta AND C. savignyi .................................... 74 4.3 DISTRIBUTION ............................................................................................... 76 4.4 OXYGEN CONSUMPTION IN Ciona spp ......................................................... 77 RESULTS ......................................................................................................................... 78 4.5 MORPHOMETRIC ANALYSES ......................................................................... 78 4.6 WATER RETENTION ....................................................................................... 82 4.7 OXYGEN CONSUMPTION ............................................................................... 84 DISCUSSION ..................................................................................................................
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